There are over 100 apps in my iTunes which I no longer want or use on my iPhone

How do I get rid of them all? Can I just delete the apps folder or will that remove them from my iphone?

If you want to delete them, right click, and select delete.
If you just want to remove them from your phone, connect your phone to iTunes, click on your device in the left pane, select apps from the device menu that pops up when you connect your device (not the left pane), select which apps you want on your phone. There is also a help tab in iTunes that will explain this.

say I have 100 apps that I deleted on my iphone but not on itunes. How do I delete them all at the same time?

One at a time in iTunes, or you may be able to select them all and then delete them. If you go to the folder where the .ipa's are stored, and delete them there, you stand a chance of corrupting iTunes.

You can't delete them from your phone and itunes at the same time unless your phone is contacted to your computer and itunes at the same time. I know its a pain to delete dumb apps one by one in iTunes but I havent figure out another way quite yet

unless you disabled the warning when you delete everything in itunes and plug your phone in it will say there are apps on your phone that are not in itunes. do you want to put them in itunes you should say yes. So the best way is to reset the warnings so it will ask.

Go to the Apps tab in the sidebar of iTunes “Click” on the app you don’t want and press the "Delete" button on your keyboard now your app will be deleted. If you want to select multiple apps at once then hold down Ctrl button while clicking and then press delete button.